Package: chimera

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chimera_1.2.0.tar.gz

StartedAt: 2013-05-01 03:33:46 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 03:48:34 -0700 (Wed, 01 May 2013)

EllapsedTime: 888.5 seconds

RetCode: 0

Status:  OK

CheckDir: chimera.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/chimera.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'chimera/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chimera' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'chimera' can be installed ... [30s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [574s/591s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotCoverage     273.906  3.110 281.174
chimeraSeqs       80.619  1.354  86.871
fusionPeptides    79.677  1.148  81.718
class.fSet        78.713  1.423  85.654
filterList        11.348  0.214  11.733
fusionName        10.296  0.165  10.657
supportingReads    8.150  0.173   8.604
importFusionData   8.082  0.173   8.383
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'chimera' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chimera)

name	user	system	elapsed
chimeraSeqs	80.619	1.354	86.871
class.fSet	78.713	1.423	85.654
filterList	11.348	0.214	11.733
fusionName	10.296	0.165	10.657
fusionPeptides	79.677	1.148	81.718
importFusionData	8.082	0.173	8.383
plotCoverage	273.906	3.110	281.174
supportingReads	8.150	0.173	8.604
tophatInstallation	0.003	0.004	0.006
tophatRun	0.022	0.012	0.035